Chemistry commons Notes - Revision history

Frodo: asdf

2024-05-02T18:01:20Z

asdf

← Older revision		Revision as of 18:01, 2 May 2024
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	[[Category:Commons]]		[[Category:Commons]]
			[[Category:Developer]]
			[[Category:Internal]]
			[[Category:Curator]]

Frodo: /* Export Chemistry Commons DB */ asdf

2024-04-09T19:32:52Z

Export Chemistry Commons DB: asdf

← Older revision		Revision as of 19:32, 9 April 2024
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	bash /nfs/home/khtang/work/gitlab/ChemistryCommons-2-0/CC_load_scripts/load_common.bash import mem2 [Reactions_Reference_Spreadsheet.xlsx]		bash /nfs/home/khtang/work/gitlab/ChemistryCommons-2-0/CC_load_scripts/load_common.bash import mem2 [Reactions_Reference_Spreadsheet.xlsx]
	=== Export Chemistry Commons DB ===		=== Export Chemistry Commons DB ===
	~~Run this script to create a snapshot of the database and JSON files~~ for ~~Enumeration~~		ssh into epyc (or any machine with postgres)
	~~bash~~ /nfs/~~home~~/~~khtang~~/~~work~~/~~gitlab~~/~~ChemistryCommons-2-0/CC_load_scripts/load_common~~.bash ~~export mem2 [destination]~~		become mtsukanov (for write permission)
			cd /nfs/exj/Fe/scripts/common_db/
			bash export_cc.bash
			(takes a couple of minutes)

			You are done!

	=== Restore data from backup ===		=== Restore data from backup ===
	psql -U commoner -d commons -p 5434 < [db_snapshot_file]		psql -U commoner -d commons -p 5434 < [db_snapshot_file]

Khtang at 19:55, 21 September 2023

2023-09-21T19:55:48Z

← Older revision		Revision as of 19:55, 21 September 2023
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	ssh epyc2		ssh epyc2
	sudo docker start chemcommons		sudo docker start chemcommons

			[[Category:Commons]]

Khtang: Created page with "== Database Management == Source chemistry commons source /nfs/soft/anaconda3/bin/activate ~khtang/.conda/envs/chemcommons === Import data from Spreadsheet === ** This will be deprecated once we switched to use postgres bash /nfs/home/khtang/work/gitlab/ChemistryCommons-2-0/CC_load_scripts/load_common.bash import mem2 [Reactions_Reference_Spreadsheet.xlsx] === Export Chemistry Commons DB === Run this script to create a snapshot of the database and JSON files for Enum..."

2023-09-20T20:57:14Z

Created page with "== Database Management == Source chemistry commons source /nfs/soft/anaconda3/bin/activate ~khtang/.conda/envs/chemcommons === Import data from Spreadsheet === ** This will be deprecated once we switched to use postgres bash /nfs/home/khtang/work/gitlab/ChemistryCommons-2-0/CC_load_scripts/load_common.bash import mem2 [Reactions_Reference_Spreadsheet.xlsx] === Export Chemistry Commons DB === Run this script to create a snapshot of the database and JSON files for Enum..."

New page

== Database Management ==
Source chemistry commons
source /nfs/soft/anaconda3/bin/activate ~khtang/.conda/envs/chemcommons
=== Import data from Spreadsheet ===
** This will be deprecated once we switched to use postgres
bash /nfs/home/khtang/work/gitlab/ChemistryCommons-2-0/CC_load_scripts/load_common.bash import mem2 [Reactions_Reference_Spreadsheet.xlsx]
=== Export Chemistry Commons DB ===
Run this script to create a snapshot of the database and JSON files for Enumeration
bash /nfs/home/khtang/work/gitlab/ChemistryCommons-2-0/CC_load_scripts/load_common.bash export mem2 [destination]
=== Restore data from backup ===
psql -U commoner -d commons -p 5434 < [db_snapshot_file]
==== How to simulate disaster ====
Stop chemistry commons docker container
ssh epyc2
sudo docker stop chemcommons

Delete database and create
psql -h mem2 -U commoner -d excipients -p 5434 //psql console login
=> drop database commons;
=> create database commons;

Restore db
psql -U commoner -d commons -p 5434 < [db_snapshot_file]

Start CC docker container
ssh epyc2
sudo docker start chemcommons